nodeScores: Node scores

In BioNetStat: Biological Network Analysis

Description

Node score (degree, betweenness, closenness, eigenvector centralities or clustering coefficient) for each network analysed.

Usage

degreeCentrality(expr, labels, adjacencyMatrix)

betweennessCentrality(expr, labels, adjacencyMatrix)

betweennessEdgesCentrality(expr, labels, adjacencyMatrix)

closenessCentrality(expr, labels, adjacencyMatrix)

eigenvectorCentrality(expr, labels, adjacencyMatrix)

clusteringCoefficient(expr, labels, adjacencyMatrix)

Arguments

expr	Matrix of variables (columns) vs samples (rows).
labels	a vector in which a position indicates the phenotype of the corresponding sample or state.
adjacencyMatrix	a function that returns the adjacency matrix for a given variables values matrix.

Value

a list of vector containing the node scores (degree, betweenness, closenness, eigenvector centralities or clustering coefficient) of each network.

Examples

set.seed(1)
expr <- as.data.frame(matrix(rnorm(120),40,30))
labels<-data.frame(code=rep(0:3,10),names=rep(c("A","B","C","D"),10))
adjacencyMatrix1 <- adjacencyMatrix(method="spearman", association="pvalue",
 threshold="fdr", thr.value=0.05, weighted=FALSE)

# Degree centrality
degreeCentrality(expr, labels, adjacencyMatrix1)

# Betweenness Centrality
betweennessCentrality(expr, labels, adjacencyMatrix1)

# Edges Betweenness Centrality
betweennessEdgesCentrality(expr, labels, adjacencyMatrix1)

# Closenness Caentrality
closenessCentrality(expr, labels, adjacencyMatrix1)

# Eigenvector centrality
eigenvectorCentrality(expr, labels, adjacencyMatrix1)

# Clustering coefficient
clusteringCoefficient(expr, labels, adjacencyMatrix1)

BioNetStat documentation built on Feb. 3, 2021, 2:01 a.m.